Lightnews — Scholar-powered news

Kirill Medvedev @kirillemedvedev.bsky.social · 26d

Really excited to be part of these Research Talks at @ucf.bsky.social Will be sharing some stories 🙂: "From Protein Domains to Cancer Subtypes: Harnessing the Power of Classification Algorithms to Advance Biology" #UCF #computerscience #bioinformatics #computationalbiology

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Reposted by Kirill Medvedev

Oded Rechavi @odedrechavi.bsky.social · 27d

BIG ANNOUNCEMENT📣: I haven’t been this excited to be part of something new in 15 years… Thrilled to reveal the passion project I’ve been working on for the past year and a half!🙀🥳 (thread 👇)

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Reposted by Kirill Medvedev

Nature @nature.com · Sep 21

Scientists have created the first ever viruses designed by AI, and they’re capable of hunting down and killing strains of E. coli

go.nature.com/4nA8E6p

World's first AI-designed viruses a step towards AI-generated life

Nature - Scientists used AI to write coherent viral genomes, using them to synthesize bacteriophages capable of killing resistant strains of bacteria.

go.nature.com

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Kirill Medvedev @kirillemedvedev.bsky.social · Sep 16

DrugDomain 2.0 (drugdomain.cs.ucf.edu) paper is out @csbj.org: doi.org/10.1016/j.cs... The new version of DB is an updated comprehensive resource, that extends earlier releases by linking evolutionary domain classifications to ligand binding events across the entire Protein Data Bank #bioinformatics

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Kirill Medvedev @kirillemedvedev.bsky.social · Aug 12

I’m happy to share that I’m starting a new position as Assistant Professor and Medvedev lab is open at the Department of Computer Science @ucf.bsky.social I am seeking motivated PhD students to join my lab. Hiring details: medvedev-lab.cs.ucf.edu/join/ Please repost 🙂 #hiring #bioinformatics

Join

Computational Structural Biology | Cancer Bioinformatics | Digital Pathology. Medvedev Lab will open in August 2025 in the [Department of Computer Science](https://www.cs.ucf.edu/) at the [University ...

medvedev-lab.cs.ucf.edu

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Reposted by Kirill Medvedev

Artem Nemudryi @artemnemudryi.bsky.social · Jul 25

First preprint from the Nemudryi Lab! 🍾

In this work, we link antiviral immunity in bacteria and humans by showing that homologs of human Schlafen nucleases protect bacteria from phages.

www.biorxiv.org/content/10.1...

Bacterial Schlafens mediate anti-phage defense

Human Schlafen proteins restrict viral replication by cleaving tRNA, thereby suppressing protein synthesis. Although the ribonuclease domain of Schlafen proteins is conserved across all domains of lif...

www.biorxiv.org

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Reposted by Kirill Medvedev

Sergey Ovchinnikov @sokrypton.org · Jul 12

Molecular cat tweezers? 😺

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Reposted by Kirill Medvedev

AI x Bio Discovery @aixbiobot.bsky.social · Jul 7

DrugDomain2.0: comprehensive database of protein domains-ligands/drugs interactions across the whole Protein Data Bank [new]
DrugDomain2.0:
Links evolutionary domain classes to ligand binding in PDB & AlphaFold human targets.

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Kirill Medvedev @kirillemedvedev.bsky.social · Jul 7

DrugDomain v2.0 is out - drugdomain.cs.ucf.edu The database reports the interactions of structural protein domains with a wide array of small organic (including drugs) and inorganic compounds, covering the full breadth of the Protein Data Bank. doi.org/10.1101/2025... #drugdiscovery #alphafold

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Reposted by Kirill Medvedev

Nature @nature.com · Jun 18

Computer algorithms have designed highly efficient synthetic enzymes from scratch

https://go.nature.com/3FLSiaS

‘Remarkable’ new enzymes built by algorithm with physics know-how

Computer approach creates synthetic enzymes 100 times more efficient than those designed by AI.

go.nature.com

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Reposted by Kirill Medvedev

Oli Clarke @olibclarke.bsky.social · Jun 12

1/x New story - the structure of the Vault cap, at 2.3Å! Matching a beautiful preprint from @sjorsscheres.bsky.social, we show that the cap of the vault particle has C13 symmetry, in contrast to the 39-fold symmetry of the body. Study lead by talented postdoc @huanli00.bsky.social from my group! ⬇️

At left, a reconstruction of the vault cap with C39 symmetry imposed; at right, the reconstruction after identifying the correct symmetry, with the three non-equivalent protomers highlighted.

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Reposted by Kirill Medvedev

Oded Rechavi @odedrechavi.bsky.social · Jun 2

One week from now!!! The craziest scientific conference ever www.the-scientist.com/a-scientific... @svobodalab.bsky.social @paveltomancak.bsky.social @zernickagoetz.bsky.social @itaiyanai.bsky.social @natanellae.bsky.social see more here
woodstock.img.cas.cz

A Scientific Conference to End All Conferences

With walk-up songs, bold ideas, and a festival atmosphere, like-minded researchers band together to reshape scientific meetings.

www.the-scientist.com

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Kirill Medvedev @kirillemedvedev.bsky.social · May 14

Thrilled to share that I'll be joining @ucf.bsky.social as an Assistant Professor.
Medvedev Lab (medvedev-lab.cs.ucf.edu) will open in August 2025. Our work will address critical biological questions in Structural and Cancer Biology. Stay tuned 😉

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Kirill Medvedev @kirillemedvedev.bsky.social · May 5

We used AI to study how post-translational modifications (PTMs) affect drug binding and protein structure. Using AF3, RFAA and Chai-1, we generated > 14,000 models with > 6,000 of ligand-related PTMs. Paper is out in J. of Chemoinformatics rdcu.be/ekFlo #drugdiscovery #alphafold #bioinformatics #AI

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Reposted by Kirill Medvedev

Trends in Pharmacological Sciences @cp-trendspharma.bsky.social · Apr 22

The cover of the April issue of @cp-trendspharma.bsky.social. Gregory Howard and William Tansey review the current status, challenges, and future prospects of cancer treatments that target the ribosome. Aberrant ribosome production and function are hallmarks of cancer.

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Reposted by Kirill Medvedev

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · Apr 17

AlphaFold is amazing but gives you static structures 🧊

In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃

Code: github.com/KULL-Centre/...
Colab: github.com/matteo-cagia...

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Kirill Medvedev @kirillemedvedev.bsky.social · Apr 11

How a junk-food splurge can change your brain activity

"Five days of indulging in chocolate bars, crisps and other junk foods can lead to lingering changes in brain activity similar to those seen in people who have type 2 diabetes"
www.nature.com/articles/d41...

How a junk-food splurge can change your brain activity

A short bout of indulgence in fatty, sugary snacks leads to lingering brain-activity changes ― even if it does not cause weight gain.

www.nature.com

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Reposted by Kirill Medvedev

RCSB Protein Data Bank @rcsbpdb.bsky.social · Apr 8

April's Molecule of the Month at PDB-101 looks at Apolipoprotein B-100 and LDL Receptor, important structures that help us better understand how "bad" cholesterol works in the body

ApoB100 (orange) wraps around the LDL particle like a belt. LDL receptors (pink and purple) bind to multiple locations on ApoB100 (PDB 9BDT).

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Kirill Medvedev @kirillemedvedev.bsky.social · Apr 2

Way to go!
This month, two journals released data from their own experiments that suggest that offering payments of around US$250 to researchers who review manuscripts speeds up the process, without affecting the quality of reviews

www.nature.com/articles/d41...

Publishers trial paying peer reviewers — what did they find?

Two journals embarked on efforts to compensate reviewers, with different results.

www.nature.com

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Reposted by Kirill Medvedev

Science Magazine @science.org · Feb 27

What do you get when #NationalProteinDay and #NationalPokémonDay meet? Pikachurin. ⚡⁠
⁠
A 2023 #ScienceSignaling study solved the structure of this extracellular protein that plays an essential role in vision.⁠ Learn more: scim.ag/4gZdRRI

Structure of the photoreceptor synaptic assembly of the extracellular matrix protein pikachurin with the orphan receptor GPR179

The structure of the orphan GPCR GPR179 bound to the extracellular matrix component pikachurin is solved.

scim.ag

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Reposted by Kirill Medvedev

Jeremy Berg @jeremymberg.bsky.social · Feb 22

I have been trying to find the time to move away from the polical hellscape we find ourselves in to finish and share a bluetorial about science.

This helps me remember what this is all about.

Ironically, it is about the treatment of pain.

the word irony is written on a white background

ALT: the word irony is written on a white background

media.tenor.com

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Reposted by Kirill Medvedev

Science Magazine @science.org · Feb 18

More and more scientists are joining the ranks of fired federal workers—and fighting back through protests, appeals, and legal challenges.

Mass firings decimate U.S. science agencies

White House dismissals and rationale challenged by dismissed scientists and lawsuits

scim.ag

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Reposted by Kirill Medvedev

Science Magazine @science.org · Feb 18

New research in Science represents a notable step forward in designing enzymes from scratch.

With a new approach, researchers designed an enzyme that uses a covalent intermediate to catalyze a two-step reaction, analogous to what many proteases do when breaking apart proteins. scim.ag/41kZBOI

Computational design of serine hydrolases

The design of enzymes with complex active sites that mediate multistep reactions remains an outstanding challenge. With serine hydrolases as a model system, we combined the generative capabilities of ...

scim.ag

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Kirill Medvedev @kirillemedvedev.bsky.social · Feb 17

Excited to share my recent research related to interactions between small molecule drugs and protein domains. @biophysicalsoc.bsky.social #bps2025 #computationalbiology #bioinformatics #drugdiscovery

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